Alignments for a candidate for glcB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Shewanella loihica PV-4

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate 5208773 Shew_1275 malate synthase (RefSeq)

Query= reanno::MR1:200654
         (549 letters)



>FitnessBrowser__PV4:5208773
          Length = 544

 Score =  916 bits (2368), Expect = 0.0
 Identities = 444/534 (83%), Positives = 481/534 (90%)

Query: 15  LNKATANGTLALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTLLAKRKDRQARIDKG 74
           +NK      L+++G  +PGQE++  EGA++LLE LC +F AEVP LL  R+ +Q  IDKG
Sbjct: 6   MNKHQLETGLSILGAPVPGQEIVLNEGALSLLEVLCDQFAAEVPKLLEMRRQKQELIDKG 65

Query: 75  ALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINALNANAKVFMADFEDS 134
           +LPDFLPETRAIRDG W+IRGIP DL DRRVEITGPV+RKM+INALNAN KVFMADFEDS
Sbjct: 66  SLPDFLPETRAIRDGDWQIRGIPQDLQDRRVEITGPVDRKMIINALNANVKVFMADFEDS 125

Query: 135 LAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICRVRGLHLKEKHVEFN 194
           LAPSW KV++GQINLRDAVRGEIEYTAPETGKHY L  +PAVLI RVRGLHLKEKHV FN
Sbjct: 126 LAPSWIKVIQGQINLRDAVRGEIEYTAPETGKHYTLDDDPAVLIARVRGLHLKEKHVAFN 185

Query: 195 QQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWAKVFAFVEERFCLQA 254
            ++IPG LFDF +YFYHNYRQLL KGSGPYFYIPKLESH+EARWWAKVFA+VEERFCL  
Sbjct: 186 GEAIPGALFDFCLYFYHNYRQLLEKGSGPYFYIPKLESHVEARWWAKVFAYVEERFCLTP 245

Query: 255 GTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKTLKRHGDRVLPDRQA 314
           GTIKCTCLIETLPAVFEM+EILYELRSNIVALNCGRWDYIFSYIKTLK+H DR+LPDRQA
Sbjct: 246 GTIKCTCLIETLPAVFEMEEILYELRSNIVALNCGRWDYIFSYIKTLKKHSDRILPDRQA 305

Query: 315 VTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNEAVLQRVRKDKELEARNG 374
           VTMD PFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKD AQNEAVL +VR DKELEARNG
Sbjct: 306 VTMDKPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDQAQNEAVLVKVRGDKELEARNG 365

Query: 375 HDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAELLKTCDGERTEQGMR 434
           HDGTWVAHPGLADTAMGIFNEYIG+DH NQLHITRDVDAPILA +LL  C+GERTE GMR
Sbjct: 366 HDGTWVAHPGLADTAMGIFNEYIGEDHVNQLHITRDVDAPILARDLLMPCEGERTESGMR 425

Query: 435 LNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHGKSLSNGKLVTKQLF 494
           LNIRIALQY+EAWI GNGCVPIYGLMEDAATAEISR SIWQWIQH + LSNGKLVTK LF
Sbjct: 426 LNIRIALQYIEAWIRGNGCVPIYGLMEDAATAEISRTSIWQWIQHEQKLSNGKLVTKALF 485

Query: 495 KDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLTLPGYEMLT 548
           K+MLVEELANVK EVG DRFTHG FTQAAVLLE+ITT+DELVDFLTLPGYE+LT
Sbjct: 486 KEMLVEELANVKLEVGPDRFTHGSFTQAAVLLEEITTADELVDFLTLPGYEILT 539


Lambda     K      H
   0.321    0.137    0.411 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1017
Number of extensions: 21
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 549
Length of database: 544
Length adjustment: 36
Effective length of query: 513
Effective length of database: 508
Effective search space:   260604
Effective search space used:   260604
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate 5208773 Shew_1275 (malate synthase (RefSeq))
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01344.hmm
# target sequence database:        /tmp/gapView.24222.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01344  [M=511]
Accession:   TIGR01344
Description: malate_syn_A: malate synthase A
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.8e-242  789.9   0.0   4.4e-242  789.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208773  Shew_1275 malate synthase (RefSe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208773  Shew_1275 malate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.7   0.0  4.4e-242  4.4e-242       1     510 [.      28     538 ..      28     539 .. 0.99

  Alignments for each domain:
  == domain 1  score: 789.7 bits;  conditional E-value: 4.4e-242
                        TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitGPvdrk 78 
                                      vl + al++l  l+ +fa+ + +ll+ r++kq  +dkg+l+dflpet++ir++dw++  ip+dl+drrveitGPvdrk
  lcl|FitnessBrowser__PV4:5208773  28 VLNEGALSLLEVLCDQFAAEVPKLLEMRRQKQELIDKGSLPDFLPETRAIRDGDWQIRGIPQDLQDRRVEITGPVDRK 105
                                      78899************************************************************************* PP

                        TIGR01344  79 mvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrprGwhlkerhle 156
                                      m+inalna++kvf+adfeds +P+w +v++Gqinl+da+rgei++t++e+gk+y+l+ + avli r+rG+hlke+h+ 
  lcl|FitnessBrowser__PV4:5208773 106 MIINALNANVKVFMADFEDSLAPSWIKVIQGQINLRDAVRGEIEYTAPETGKHYTLDDDPAVLIARVRGLHLKEKHVA 183
                                      ****************************************************************************** PP

                        TIGR01344 157 idgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprGtikatvlietlpaaf 234
                                       +g+ai+g+l+df lyf+hn r+ll+kG+GPyfy+Pklesh+ear+w  vf + +e + l  Gtik t lietlpa+f
  lcl|FitnessBrowser__PV4:5208773 184 FNGEAIPGALFDFCLYFYHNYRQLLEKGSGPYFYIPKLESHVEARWWAKVFAYVEERFCLTPGTIKCTCLIETLPAVF 261
                                      ****************************************************************************** PP

                        TIGR01344 235 emdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGmaafi 312
                                      em+eilyelr  ++ lncGrwdyifs+ik+lkk+++++lPdr+avtmdk+fl+ays+lli+tch+rga a+GGmaafi
  lcl|FitnessBrowser__PV4:5208773 262 EMEEILYELRSNIVALNCGRWDYIFSYIKTLKKHSDRILPDRQAVTMDKPFLSAYSRLLIKTCHKRGALAMGGMAAFI 339
                                      ****************************************************************************** PP

                        TIGR01344 313 PikddpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge..pnqldrvrledvsitaaellevkd 388
                                      P+k d+a nea+l kvr+dke+ea+nGhdGtwvahP+l+++a+ +f+e++ge   nql+ +r++d++i a +ll  ++
  lcl|FitnessBrowser__PV4:5208773 340 PAK-DQAQNEAVLVKVRGDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGEdhVNQLHITRDVDAPILARDLLMPCE 416
                                      ***.9*********************************************997789********************** PP

                        TIGR01344 389 asrteeGlrenirvglryieawlrGsGavpiynlmedaataeisraqlwqwikhGvvledGekvtselvrdllkeele 466
                                      ++rte G+r nir++l+yieaw+rG+G+vpiy lmedaataeisr+++wqwi+h + l++G+ vt++l++++l eel+
  lcl|FitnessBrowser__PV4:5208773 417 GERTESGMRLNIRIALQYIEAWIRGNGCVPIYGLMEDAATAEISRTSIWQWIQHEQKLSNGKLVTKALFKEMLVEELA 494
                                      ****************************************************************************** PP

                        TIGR01344 467 klkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                      ++k e+g ++++++ +++aa lle++++++el dfltlp+y+ l
  lcl|FitnessBrowser__PV4:5208773 495 NVKLEVGPDRFTHGSFTQAAVLLEEITTADELVDFLTLPGYEIL 538
                                      ******************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (544 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 13.02
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources